plot_seasonality {GHRexplore} | R Documentation |
Seasonality plot
Description
Plots yearly time series of covariates, case counts, or incidence rates to explore seasonality patterns.
Usage
plot_seasonality(
data,
var,
time,
type = "cov",
pop = NULL,
pt = 1e+05,
area = NULL,
aggregate_space = NULL,
aggregate_time = "month",
aggregate_space_fun = "mean",
aggregate_time_fun = "mean",
transform = "identity",
title = NULL,
var_label = NULL,
ylab = NULL,
xlab = NULL,
free_y_scale = FALSE,
palette = "IDE1"
)
Arguments
data |
Data frame containing equally spaced (daily, weekly, monthly) covariate or disease case observations for one or multiple locations. |
var |
Name of the column identifying the variable to be plotted. |
time |
Name of the variable that identifies the temporal dimension of the data frame. Its values must be in date format ("yyyy-mm-dd") representing the day of observation for daily data, the first day of the week for weekly, or the first day of the month for monthly observations. |
type |
Character that specifies the type of variable in |
pop |
Character identifying the variable name for population. Only needed
if |
pt |
Scale of the person-time (default 100,000) for incidence rates. |
area |
Name of variable that identifies the different locations (e.g., areal units) for which a time series is available. |
aggregate_space |
Name of variable used to define spatial aggregation groups. |
aggregate_time |
Temporal scale used to perform temporal aggregation. Options are: "week" (ISO 8601), "month", "year". |
aggregate_space_fun |
Character indicating the function to be used
in the aggregation over space for |
aggregate_time_fun |
Character indicating the function to be used
in the aggregation over time for |
transform |
Character, defaults to "identity" (i.e., no transformation).
Transforms the y-axis for better visualization. Useful options include
"log10p1" |
title |
Optional title of the plot. |
var_label |
Character with a custom name for the case or covariate variable. |
ylab |
Label for the y-axis. |
xlab |
Label for the x-axis. |
free_y_scale |
If TRUE, the y-axis scale is free in each facet. |
palette |
GHR, RColorBrewer or colorspace palette. Use "-" before the palette name (e.g., "-Reds") to reverse it. |
Value
A ggplot2 seasonality plot.
Examples
# Load data
data("dengue_MS")
# Seasonality plot of a covariate with space aggregation
plot_seasonality(dengue_MS,
var = "tmax",
time = "date",
var_label = "Max temp.",
type = "cov",
area = "micro_code",
aggregate_space = "region_code")
# Plot case counts (log scale) with space aggregation
plot_seasonality(dengue_MS,
var = "dengue_cases",
time = "date",
type = "counts",
area = "micro_code",
aggregate_space = "meso_code",
transform = "log10p1",
var_label = "Monthly Dengue Cases",
xlab = "Month",
ylab = "Number of cases",
free_y_scale = TRUE)
# Seasonality plot of incidence
plot_seasonality(dengue_MS,
var = "dengue_cases",
time = "date",
type = "inc",
pop = "population",
area = "micro_code",
pt = 1000,
title = "Monthly Dengue Incidence",
palette = "Reds")